More than two years after breaking ground for its new $275 million home in downtown Miami, the Patricia and Phillip Frost Museum of Science said Friday it fired the company in charge of managing the complicated construction project.

Representatives for the museum, which is using $165 million in county bond money, said they had ended the relationship with Boston-based Suffolk Construction and chosen Skanska USA to oversee construction moving forward.

“We just felt the decision was in the best interest of the project after a long and careful process and a lot of reflection,” said museum president and CEO Gillian Thomas, who said the construction is about half complete.

Museum officials said Friday they planned to proceed with “minimal interruption” and did not foresee additional delays or significant budget changes associated with the switch. While the earliest plans called for the science museum to open by the end of 2014, recent expectations have suggested the site might be ready to host a party at the end of 2015. Thomas said she expects a more definitive timeline by September.

Thomas did not reveal the issues that led to the termination, but monthly progress reports to the county show signs of strain with Suffolk emerging as far back as a year ago. More recent reports also outlined concerns about brick-and-mortar challenges with walls, columns and slabs of a complex project that includes a 3-D planetarium, a 600,000-gallon aquarium and an energy playground.

Jeffrey A. Gouveia Jr., Suffolk’s executive vice president, said problems arose due to design deficiencies that repeatedly forced the company to turn to architects for additional information before they could proceed.

“The systems in the building, the structure of the building and the architecture of the building are not fully coordinated in the design such that we would be able to build it in an efficient manner,” he said.

Gouveia said those issues led an eight-month period at the Museum Park site last year when “virtually nothing” got done.

“It just took quite a while for a lot of these issue to be resolved so that we would actually get something we could build,” he said. Lead design firm, London-based Grimshaw Architects, could not be reached late Friday for comment. Local architect Raul Rodriguez, principal of Rodriguez & Quiroga, said, “There is a tri-partite effort: owner, architect, contractor. The owner decided to terminate the contractor.” He declined to elaborate.

While museum officials said the site “has remained fully operational since the day construction started,” the monthly reports to the county reveal frequent frustration over holdups.

“Some delays due to coordination issues are occurring,” the May/June 2013 report begins. The next report, from July, said construction work had resumed, though it's unclear for how long it had been stalled.

Subsequent reports through the end of 2013 note efforts to accelerate construction. By October, a new consultant, Hill International, had been appointed to replace former project management firm Oppenheim Lewis.

While January’s report noted that construction was speeding up and manpower had been increasing, “not as much happened over the year end as had been anticipated and in fact promised.” Museum officials complained about Suffolk failing to produce a schedule in February 2014 — and in March, said they had begun the process of notifying the company of the intent to terminate the agreement.

That notice of termination was delivered Thursday afternoon. Skanska, a firm with headquarters in New York that bid for the original construction management contract in 2010, was on site Friday. Museum chief operating officer Frank Steslow said there was minimal construction activity at the site adjacent to the Pérez Art Museum Miami on Friday, but work was expected to resume Saturday.

“Keep in mind that this is probably for the most part an administrative change,” Steslow said. “The people building the project are still building the project.”

But Suffolk’s Gouveia, who said the termination was a first for the company, took issue with that characterization, calling the change “a huge deal.” Suffolk had 36 people working on the project.

“When you think about all of the knowledge of a very large staff that is now gone, that knowledge doesn’t transfer,” he said. “It’s in their minds and in their actions.”

County Mayor Carlos Gimenez said Friday he learned of the imminent Suffolk dismissal earlier this week.

The county has had experience with changing construction companies midway through a project — namely at Miami International Airport, a massive undertaking that had been plagued by overruns and delays before it was wrested under control.

“They're going to have the new contractor in, trying to take over as many of the subs as possible and then move forward,” Gimenez said of the museum. “That's a very difficult process. We know firsthand from when it happened at MIA...There are always issues when that happens.”

Steslow said all subcontractors are expected to be briefed by Monday and that as of Friday, every company that started with the project remained.

But the Miami Herald obtained an email from one subcontractor sent Friday morning to Suffolk executives.

“Suffolk was the glue holding this project together,” the subcontractor wrote. “We absolutely do not want to work for this owner or any of their representatives.”

Throughout this period of contention, all work was verified as “satisfactory’’ by the museum before the county agreed to pay, said Michael Spring, director of Miami-Dade's Department of Cultural Affairs.

The under-construction science museum has so far submitted more than $91 million in invoices to the county, which according to the Miami-Dade budget office has paid out nearly $88 million.

“We got assurances they were not paying for work that was unsatisfactory and needed to be fixed,” Spring said. He also warned Thomas that no money beyond the bond amount will be released if the museum’s costs increase.

“You realize that the county’s commitment of $165 million has a period after it,” he said he told her. “There is no more money from the county for the project. If any of this costs you more money, it’s money you have to raise. Her response was: ‘We understand that perfectly.’”

So far, the fundraising efforts have brought in about $86 million, Thomas said Friday.

“This is a real public-private partnership all committed to doing the best job we can with the public money and private money,” she said. “We’re aware it’s something we have to do very carefully and very well.”